Blages

Monday, January 31, 2011

So, this will be a non-science Egypt Week post. Opposition organizers in Egypt have called for a massive protest on Tuesday, anticipating that millions will march on Tahrir Square in the morning. Here is hoping that this leads to better things.

Below is the text of the Langston Hughes poem I, Too, Sing America. While it was obviously written in the context of racial dynamics and inequality in the United States, its sense of hope, defiance, and the inevitability of justice speaks for oppressed and dismissed people everywhere.

I, too, sing America.

I am the darker brother.
They send me to eat in the kitchen
When company comes,
But I laugh,
And eat well,
And grow strong.

Tomorrow,
I'll be at the table
When company comes.
Nobody'll dare
Say to me,
"Eat in the kitchen,"
Then.

Sunday, January 30, 2011

So, our next Egypt Week feature is a theoretical paper on a topic closely related to the last post. Once again, we are interested in understanding the mechanisms that are responsible for encouraging or enforcing cooperation, thereby facilitating collective action. Last time, we talked about a paper that found that "altruistic" or "third-party" punishment is common in large-scale, complex societies, but is rare in small-scale societies, while "spiteful" punishment is universal.

Many empirical and theoretical studies of cooperation focus on punishment as a mechanism for enforcing societal norms. Basically, you set up a situation where the group benefits if people cooperate, but each individual benefits by not cooperating. If mechanisms exist to punish people for not cooperating, you get cooperation. Which is to say that the existence of punishment changes the individuals' incentives. The benefits of not cooperating are outweighed by the cost of being punished. No big mystery there.

But what if punishment itself is costly? Punishment can stabilize cooperation, but what stabilizes punishment? Some models rely on an infinite succession of punishments, where people punish people who fail to punish people who fail to cooperate, and people punish people who fail to punish people who fail to punish people who fail to cooperate, and people punish ... well, you get the idea.

Today's paper asks if cooperation can be enforced by corrupt punishment. That is, while punishment is still treated as costly, punishers are not necessarily cooperators themselves, as is commonly assumed in models of this sort. Furthermore, the corrupt punishers ("policers") suffer a lower cost when punished than do non-punishers ("civilians").

A corrupt policer looks forward to a cushy retirement, thanks to his hypocritical enforcement of others' cooperation. Little does he suspect how a new, young partner, who colors outside the lines, but has a heart of gold, will turn his whole life upside-down, with hilarious consequences.

The model shows that in the presence of a modest power imbalance, cooperating civilians and corrupt policers can coexist. That is, a moderate level of corruption is consistent with, and can even stabilize cooperation. However, when the power imbalance becomes large, corrupt policers overrun the population, the system breaks down, and cooperation is lost.

The first part of the result is nice because it provides a degree of robustness to the "cooperation through punishment" paradigm, as it does not require the punishers to be acting altruistically themselves.

The second part of the result is perhaps more directly relevant to Egypt Week. Societies can function in the presence of a degree of inequality, and they can tolerate a certain amount of hypocrisy from their leaders. But too much hypocrisy and inequality is inconsistent with the type of collective action that governments are meant to facilitate.

It is heartening to see that when a less corrupt alternative presents itself, people are still capable of collective action on a massive scale.

[1] This is an online, ahead-of-print publication, which is why there are no page numbers, but it should be findable through the DOI.

[2] Disclosure: The first author on this paper is a long-time friend and colleague, and we have worked together on issues of intragenomic conflict. Here is photographic evidence of our friendship, from when we were traveling around Lyon, France like Thelmo and Louis following the 2010 SMBE meeting:

On our way to the Palais de Justice, we accidentally activated our Wonder-Twin Powers. Francisco took the shape of an evolutionary biologist, and I took the form of a French trash can. Photo by Gleek.

So, welcome to the first Egypt Week edition of Lost in Transcription. We're going to kick it off with an anthropology paper that uses a cross-cultural approach to study the origins of human punishment and cooperation.

If you're not familiar with this vein of research, let me set the stage for you. The "problem" of cooperation when people talk about it in anthropology, biology, and economics is this. If you take a super naive view of natural selection, it would say that we should have evolved to ruthlessly pursue our own self interest. In particular, if we have an opportunity to cheat and get away with it, the logic of self interest suggests that we should. From this perspective, the whole idea of successfully engaging in collective action seems absurd.

Contrary to this naive expectation, we observe that people do forego opportunities to pursue their own narrow self interest, and the history of civilization is one of successful collective action on an enormous scale.

Saturday, January 29, 2011

So, unless you are in China, you are undoubtedly aware of the massive protests that have been going on in Egypt for the past few days. If you're like me, you are filled with a mixture of hope and anxiety. I sincerely hope that the Egyptian people will be able to establish a new government that is actually responsive to their needs, and that it can be done with a minimum of bloodshed. But I also know that it is possible that this ends with a brutal crackdown and the Egyptian government resuming business as usual.

Also, if you're like me, you feel a sense of solidarity with the protesters, but feel completely powerless to do or contribute anything. I am thousands of miles away, and do not have any inside information or clever insights on Egyptian politics and culture. I am a poet and a theoretical evolutionary biologist – two things that find little practical application even in the best of circumstances.

Still, I feel that I want to do something, so I will do what I know. I am going to dedicate this week's blog entries to the protesters in Egypt and to people everywhere who long for more freedom and better government. Topic-wise, I will discuss a number of recent scientific papers from the evolutionary literature on cooperation, punishment, and corruption.

I have no illusion that this can have any impact on the course of events in Egypt, or on the protests in Jordan, Yemen, and elsewhere. I simply hope that I can contribute something to the knowledge that we are all in this together.

The desire for freedom and safety and a better life for ourselves and our children is not defined or limited by nationality or religion or race or language. As an American, I am fully aware that my government's rhetoric about freedom and democracy is often at odds with its support of corrupt and anti-democratic regimes, including Mubarak's. But a government is rarely the same thing as a people. All of the people I have spoken with, American and not, are hoping and praying that this will be a turning point in history, and that the people of Egypt (and Iran and Myanmar and Uganda and on and on) can move forward together into a better future.

Friday, January 28, 2011

So, you may have heard about Tihomir Petrov, the math professor at Cal State, Northridge who was arrested for urinating on his colleague's office door. Campus security got video footage of Petrov in the act when they set up video cameras following the discovery of "puddles of what they thought was urine."

You may be asking yourself, what the heck was this dude thinking? How should we interpret the behavior of this Homo mathematicus (not that there's anything wrong with it) specimen?

What Professor Petrov was probably thinking.

Fortunately, once again, Science!™ has an answer for you. Urine is commonly used as a scent marker to deter competitors. But deter them from what? Traditionally, it has been assumed that scent marking is primarily used to defend territory against intruders, thereby safeguarding resources such as food and space. However, some recent studies have suggested that scent marking may be used to defend mates and mating opportunities. One of the difficulties in studying such a question, however, is that in many systems, competitors for territory and competitors for mates are the same individuals.

A recent study by a group of researchers in the UK, Uganda, and Switzerland have attempted to separate out these two forms of competition in a study of the wild banded mongoose. This species lives in large social groups that share a territory. Thus territorial competition occurs primarily between different social groups, whereas competition over mates occurs primarily within groups.

The researchers found that the mongoose populations marked uniformly throughout their territory, and did not appear to increase the frequency of marking in those regions where two territories overlapped. This suggests that, in this species at least, defense of mates and mating opportunities represents a major contribution to scent-marking behavior, perhaps more so than territorial defense.

So, can we extrapolate from the behavior of the wild banded mongoose to the behavior of wild banded mathematician Tihomir Petrov? Of course we can! Should we extrapolate? Absolutely not! But, here at Lost in Transcription, we're all about the possible, so here is the take-home message. Castle and Beckett should look beyond professional disputes between the two mathematicians. They need to be looking at the love-triangle angle (Love angle4?) for motive.

Alternate theory: As Northridge is, like, the pr0n capital of the country, Petrov might not have been the original urinator. When he saw that the cameras had been set up, he might have assumed that he had been cast in a movie, and that peeing on the floor was what was expected of him. Just sayin'.

Thursday, January 27, 2011

So, we've already discussed the fact that genomic imprinting is mediated through epigenetic differences between the maternally and paternally inherited gene copies. That is, at an imprinted locus, the maternally inherited allele will have one pattern of epigenetic modifications, while the paternally inherited allele has a different pattern. These differences are first established in the male and female germ lines, when the alleles that will eventually become maternally and paternally derived are in physically different locations. It is not hard to imagine, then, how these differences could be established. One pattern of gene expression in spermatogenesis results in the paternal-specific epigenetic modifications. A different pattern of gene expression in oogenesis results in maternal-specific epigenetic modifications.

But what are these epigenetic modifications, and how do they change the expression pattern of the gene?

There are a number of modifications involved in imprinting, but for the moment, we're going to focus specifically on the simplest and best-understood mechanism: DNA methylation.

The two horizontal lines in this picture represent the two copies of a gene. The big, solid box is the part of the gene that actually codes for the protein. The open box is the promoter region, which is the part of the DNA sequence responsible for regulating expression of the gene. The lollipop things indicate DNA methylation on cytosine residues (the "C" of the A, C, G, T alphabet that makes up DNA).

In this simplest type of scenario, the DNA sequence in the promoter region binds to a variety of proteins that recruit the molecular machinery that will transcribe the gene, leading eventually to production of the corresponding protein. The addition of methyl groups to the DNA changes its binding properties, so that it no longer binds to this machinery, and that copy of the gene is not transcribed.

If you're not a molecular biologist, you can think of it like this. The transcription machinery is a bit like a Xerox machine, and the gene is like the master copy of some document. The promoter region is like a lock that has to be unlocked before you can copy this particular document. There are a number of proteins called "transcription factors" that function like a key to this lock. These transcription factors fit nicely on the promoter region, unlocking the gene and resulting in the production of many copies of the gene product.

Adding methylation to the promoter region is a bit like squirting epoxy into the lock. The presence of the methyl groups actually changes the physical shape and chemical properties of the DNA. So, when you try to put the key in, it no longer fits right, and the gene can not be copied.

In the top part, we see the red transcription factor binding to the black promoter region, which will activate transcription from the gene. In the bottom part, methyl (CH3) groups have been chemically added to the promoter region, preventing binding, and thereby preventing transcription.

So, these relatively subtle chemical changes are able to completely alter the functional properties of the gene.

Next time, we'll talk about how these methylation patterns are maintained through development, and how the two gene copies are able to maintain distinct epigenetic states across multiple rounds of cell division and DNA replication. Make sure to tune in, because it's really slick!

The two references represent the first proposals that DNA methylation might be the thing that permits the stable transmission of patterns of gene expression across cell divisions.

Sunday, January 23, 2011

So, I'm among those who believe that a baseball player only gets a reputation for being "scrappy" if they are not very good. You only get called scrappy if you scramble around and smother a ground ball that a fielder with better range would have gotten to easily. (I'm looking at you, David Eckstein.)

I decided to address this question by collecting some data that really has nothing to do with the original question. Using a method similar to that used by the Negative Log Google Naked Ratiometer, I looked at each position to see how often the position was referred to as "scrappy" and how often it was referred to as "crappy."

For example, the Log Scrappiness for second basemen is calculated by taking the logarithm (base 10) of the number of google hits for "scrappy second baseman" divided by the number of hits for just "second baseman." Similarly for Log Crappiness. Positions are more often referred to as "crappy" if they are higher on the graph. They are more often "scrappy" if they are further to the right.

If we look at the infielders and outfielders separately, the positions fall close to two straight lines with similar slopes.[1] Within each group, the relative scrappinesses are more or less what you might expect. The interesting thing is that each group has an inverse relationship between scrappiness and crappiness.[2] The scrappier a position is, the less crappy it is.

The solid diagonal line is the iso-(s)crapocline, or the line indicating equal scrappiness and crappiness. First basemen (1B), left fielders (LF), and right fielders (RF) are crappier than they are scrappy. Third basemen (3B), shortstops (SS), second basemen (2B), and center fielders (CF) are more scrappy than crappy.

Pitchers and catchers were left off, since there is too much cross talk on Google with non-baseball uses.

But, let's get back to the original question: "Can you spell scrappy without crappy?" One answer is, "Yes, if you spell it in Albanian." Via Google Translate: you can definitely spell i copëzuar without i mutit.

[1] You may have noticed that these straight lines represent power laws. If I were a physicist, I would say something about universality classes, and publish this blog post in Physical Review E.[3]

[2] This seems to violate the assertion I made at the beginning of the entry, but the right way to do address that question would actually be to look at how often "scrappy" is used to describe individual players, and then to compare this to an objective measure of crappiness, based on player statistics.

Friday, January 21, 2011

So, a lot of people have been making predictions recently about how the world is going to end, or when the rapture is going to start, or what will be the new vampire. It all just gets so gosh-darned confusing!

Never fear! I have produced this handy-dandy Venn diagram that graphically tells you what things could, conceivably happen in 2012, and which of those things actually will happen:

So, in the previous installment, we introduced the "Loudest Voice Prevails" principle, which describes the evolutionarily stable pattern of gene expression at an imprinted locus where there is an intragenomic conflict over the total level of gene expression. Basically, the allele that favors lower expression becomes transcriptionally silenced. Expression from the other allele (the "louder" voice) evolves to the level that maximizes its inclusive fitness. In this sense, the active allele at an imprinted locus "wins."

But what is going to happen if we have a pair of imprinted genes that exert opposite effects on the phenotype? If we have a paternally expressed growth enhancer, it will evolve to bring the growth phenotype up to the paternal optimum. If we have a maternally expressed growth suppressor, it will evolve to bring the growth phenotype down to the maternal optimum. But what if we have both?

Well, intuitively, if there is conflict between maternally and paternally derived genes over the optimal growth phenotype, then the phenotype can't simultaneously satisfy the paternal and maternal optima. One or the other (or both) of these genes will always be under selection to increase its gene expression level (or, equivalently, the activity or longevity of the gene product, etc.). Thus, these two opposing genes will become involved in a kind of arms race.

In the simplest possible model that we can write down, this arms race goes on indefinitely, with natural selection driving each of the genes towards infinite expression. Clearly, in a real biological situation, this will not be the case, and something will step in to bring this escalation to a halt. The questions then become: What stops the escalation? And, what does the system look like at its new, escalated, evolutionarily stable state?

To think about this, let's return to our analogy from last time, where Pat and Chris are sharing an office, but disagree about what temperature the office should be kept at. Recall that genes are totally passive aggressive, so Pat and Chris don't compromise or communicate. They just use the tools at their disposal to move the office closer to their preferred temperature. Pat wants the office at 71 degrees. Chris wants it at 70.

We saw that if Pat and Chris both have space heaters, eventually Chris's space heater is off, while Pat's holds the temperature at 71. On the other hand, if they both have air conditioners, Pat will turn his/her A/C off, and Chris will get to have the room at 70.

If each of them has a space heater and an air conditioner, we have an arms race on our hands. Whenever the temperature is below 71, Pat will turn up the space heater. Whenever it is above 70, Chris will turn up the air conditioner. In passive-aggressive-allele fashion, this will go back and forth until the space heater and air conditioner are both blasting away. In the absence of any constraints or side effects, it will go on until both are blasting away infinitely.

There are several ways that the escalation could stop, however, each of which has a biological analog.

(1) Mechanical limitation. There will be some limit beyond which gene expression / activity can not increase. Once one of the genes reaches its limit, the other will win. Like if Pat's Tufnel-brand space heater goes to eleven, Pat wins. Of course, this will depend on the mechanisms through which the two genes exert their influence. For instance, if Chris's air conditioner is actually a combination air conditioner / food processor / exfoliator, Chris might have to turn it way way up to get the air conditioning equivalent of a little bit of space heating. Similarly, a gene product might perform multiple tasks, and this pleiotropy could limit its competitive ability in the arms race.

(2) Production costs. One difference between the single-locus solution and the two-locus solution is the level of energy consumption. If Chris's space heater is off, Pat's holds the temperature at 71. If Chris's air conditioner is maxed out at ten, Pat's space heater (which goes to eleven, remember) holds the temperature at 71. The difference is that the second solution comes with a huge-ass electricity bill. Can this sort of cost actually halt the escalation? Maybe. This requires either that there are diminishing returns to increased escalation, or that there are accelerating costs to production (like utility rates where your thousandth kilowatt-hour costs more than your first one).

(3) Intervention. In a real office, we might expect that the manager would come in and yell at Pat and Chris, telling them to turn down their space heater and air conditioner. Maybe the manage would mandate an office temperature of 70.5 degrees. Does this ever happen with genes? Could a consortium of unimprinted genes step in and stop the escalation? There is no evidence to my knowledge of such things happening in the context of genomic imprinting, but this type of intervention is thought to be responsible for meiotic sex-chromosome inactivation, where the autosomes all gang up and put the sex chromosomes in a headlock in order to prevent meiotic drive.

(4) Side effects. What if turning up Pat's space heater also makes the music louder in the office? What if Chris's air conditioner draws so much power that it causes occasional brown-outs? This is the other way in which the escalation between imprinted genes might be self limiting. If we consider a monolithic "growth phenotype" in isolation, then each allele has a simple, monolithic optimum. But genes are seldom like that. A paternally expressed allele may benefit from increased expression due to the effect of that increased expression on growth. But what if that increased expression has other consequences, as well? Maybe those other effects are detrimental to the allele's inclusive fitness. If those deleterious side effects outweigh the growth-related benefits, then natural selection will not drive further escalation.

In future installments, we'll look at some specific examples of escalating genes. But first, we'll step back and look at some of the other features and consequences of imprinted genes.

Wednesday, January 19, 2011

So, for those of you who know us personally, this will not come as a surprise, because you already know that my wife is a hundred times smarter and more talented than I am. But here's the new news. She has just sold her book manuscript, Remarkable, to Dutton publishing as part of a two-book deal. Other authors in their list includes authors ranging from Ken Follett and Eckhart Tolle to John Hodgman and Jenny McCarthy. Their backlist includes, among other classics, the Winnie-the-Pooh books.

Remarkable is a middle-grade reader, which, as I understand it, is the age group just below young adult. I think that this is approximately the same group as the Harry Potter and Percy Jackson books. Or, if you're actually familiar with the genre, the Mysterious Benedict Society books.

I don't want to give anything away, other than to say that it is the BEST FREAKING BOOK YOU WILL EVER READ IN YOUR LIFE, EVER. The target age group is, technically, 9-12, so buy it for your kids. But, like all the best children's literature, it has layers of nuance in its themes and characters that will engage adult readers.

Obviously, I'm not an unbiased reviewer here, but this book moved to tears and to laugh out loud – sometimes at the same time – and even after reading multiple previous drafts.

For those in the population genetics community, you can look forward to a cameo appearance by John Novembre.

The editor is hoping to include the book in Dutton's Spring 2012 catalog. When more information becomes available, I'll pass it along.

If you're connected to her on Facebook or Twitter, say hi and congratulations, because she'll no doubt be too modest to adequately blow her own horn (yet another way in which she is a hundred times better than I am). Or, stop by her sadly neglected blog and say hi in the comments.

From me, congratulations Lizzie K. Foley!! You deserve everything good that is coming to you. And congratulations to her agent, Faye Bender, and her brand-new editor, Nancy Conescu!

Tuesday, January 18, 2011

So, what do you do with the two guys who wrote the screenplay for Yogi Bear, which was filmed in approximately three too many dimensions and made as much money as sense? Well, if you're Dreamworks, you pay them to make another fifty-year-old cartoon into a movie. Or rather, a cartoon that was part of another cartoon. And then you cast Robert Downey Jr. as a dog. Presumably because his complete lack of talent complements the complete lack of creativity at the studio.

Following similar logic, I assume that the soundtrack will be composed by feeding beans to a room full of monkeys.

The movie will be based on Peabody's Improbable History, which was a regular feature on The Rocky and Bullwinkle Show. In it, Mr. Peabody, a bespectacled dog-genius, and his sidekick, Sherman, a bespectacled boy-not-genius, use the WABAC machine to travel back in time and visit famous historical events.

The historical events in question unfold in humorous ways.

To be fair, this was the second best segment on the show, after Bullwinkle reading poetry. But still, why would Dreamworks do this? With real money that could have been better spent feeding the poor, or, if we're honest, teaching the poor Esperanto?

Monday, January 17, 2011

So, you may be familiar with the opening of Nietzsche's Also sprach Zarathustra, where he describes the three metamorphoses: spirit becomes camel, camel becomes lion (and slays dragon), and lion becomes child. I think that Nietzsche's metaphor works really nicely in a lot of circumstances. I most strongly associate it with biology graduate training, but I think that similar reasoning probably applies in a lot of other fields.

In the early stages of education, through high school and college, and into the beginning of graduate school, the student is like the camel, who has to develop a strong back by learning to carry all of the received knowledge. Then, starting typically in grad school, you learn that all of the things that are in the textbooks you've been using are not strictly true. This is like the transformation into the lion, who has to slay the dragon covered with scales, where each scale has golden letters that read "Thou Shalt!" It is only after passing through these two stages that the third transformation occurs (maybe while you're a postdoc?), where the lion becomes the child. The child is innocence and creativity, and it is this child who advances knowledge by possessing skills and knowledge, but no longer being beholden to them.

Now, one of the problems with the system is that not everyone makes it all the way through the transformations. Many scientists never fully shed the camel phase. They are quite skilled at the type of incremental research that NIH and NSF love to fund, and are often successful, but are excessively (IMHO) tied to the dogma and assumptions that define their discipline.

Other people get stuck in the lion phase. These are the compulsive paradigm shifters. They are Don Quixotes who spend their lives slaying imaginary windmill-dragons. In evolutionary biology this is the phenomenon responsible for the perennial "Darwin was WRONG!!" headlines.

That last step is really the hardest one. It requires us to recapture the innocence and creativity of childhood, but to wield it tempered with skill and knowledge. Unfortunately, the implementation of most science education is such that the camel and lion stages are coupled with a soul-crushing strangulation of the childlike curiosity that we are all born with.

So, what does this all have to do with Axe Cop? Axe Cop is a web comic (and now a book) written by a pair of brothers, Ethan and Malachai Nicolle. The twist? Ethan is 29 years old, and Malachai is 5. Ethan has clearly absorbed the illustrating and storytelling skills of the comic-book camel, and has slain the comic-book dragon. The comic itself is just bursting with a child-like creativity that is easy to recognize but difficult to produce. How do they do it? I suspect that Ethan was able to retain and/or recapture his creativity and innocence better than most, but the biggest thing is probably the co-authorship with Malachai, who has not yet entered the camel phase.

There is undoubtedly a lesson here about how to do great science, although I can't quite figure out the mechanics. One possibility is this.

36 "but bout dat dai or hour no wan knows, not even teh angels in heaven, nor teh son, [e] but only teh fathr.37 as it wuz in da dais ov noah, so it will be at teh comin ov teh son ov man.38 4 in da dais before teh flood, peeps wuz eatin an drinkin, marryin an givin in marriage, up 2 teh dai noah enterd teh ark;39 an they knew nothin bout wut wud happen til teh flood came an took them all away. Dat iz how it will be at teh comin ov teh son ov man.40 2 doodz will be in da field; wan will be taken an teh othr left.41 2 women will be grindin wif hand mill; wan will be taken an teh othr left.42 "therefore keep watch, cuz u do not knoe on wut dai ur lord will come.43 but understand dis: if teh ownr ov teh houz had known at wut tiem ov nite teh thief wuz comin, he wud has kept watch an wud not has let his houz be brokd into.44 so u also must be ready, cuz teh son ov man will come at an hour when u do not expect him.

Sunday, January 16, 2011

So, it's been a while since the last installment of the Primers on Imprintingfeature, but they should be posted with greater regularity in the upcoming weeks. This time we're going to introduce something that we will see again in future installments: small differences in selection lead to large differences in behavior.

Last time, we introduced the most widely discussed and most successful explanation of the evolutionary origins of genomic imprinting, the "kinship" or "conflict" theory. According to this theory, imprinted gene expression is a consequence of the fact that natural selection acts differently on alleles depending on their parent of origin. There are several ways to think about the origin of this differential selection, but we talked about it in terms of the framework that I find most intuitive: inclusive fitness.

As we also noted last time, even in the cases where the asymmetry in selection on maternally and paternally derived alleles is sufficiently large to drive the evolution of imprinted gene expression, the actual magnitude of this asymmetry is actually incredibly small. Why? Well, even for a allele with large effects on the survival and reproduction of related individuals, the dominant factor in the inclusive fitness of that allele is still going to be the survival and reproduction of the individual organism carrying that allele around.

But, the standard pattern observed with imprinted genes is that the allele-specific expression is all or nothing. For example, an allele might be expressed when it is inherited from a male, but completely silent when inherited from a female. So this small difference in the optimal expression levels of the maternally and paternally derived alleles leads to – in a way – the largest possible difference in the realized expression levels of the two alleles.

I like to think of this in terms of an analogy. Imagine that Pat and Chris share an office, and that they have a slight disagreement over the temperature they want the office at. Say Pat wants the office to be at 71 degrees (Fahrenheit), while Chris wants it to be 70. Each of them has control over a small space heater, and this is the only mechanism that they have for manipulating the temperature. [1]

What's going to happen? Let's say the temperature is 70 degrees. Pat will turn up his/her space heater until the temperature reaches 71. In response, Chris will turn his/her space heater down until the temperature comes down to 70. They will go back and forth like this until, eventually, Chris's space heater is completely turned off. Pat will then turn his/her space heater up to get the room to 71. Then we're done. Chris is unhappy about the temperature of the room, but no longer has any ability to make it any cooler.

Two things about this outcome. First, a small disagreement over the ideal temperature has led to a large divergence in the strategies: Chris's space heater is all the way off, while Pat's is on and doing all the work. Notice that the outcome would be exactly the same, in principle, if Chris's ideal temperature were 70.9 degrees, or even 70.999 degrees. [2]

Second, Pat wins. This is a consequence of the fact that we are talking about space heaters, and that Pat prefers the higher temperature. If, instead of space heaters, Pat and Chris each had control of an air conditioner, Chris would be the winner. At equilibrium, Pat's air conditioner would be all the way off, and the room would be at 70 degrees.

This is also the way it works with alleles at an imprinted locus. Let's consider the case of a gene where increased expression results in increased prenatal growth. The inclusive fitness argument says that the optimal amount of this growth factor is higher for an allele when it is paternally inherited than when it is maternally inherited. Say this patrilineal optimum is 105 units, while the maternal optimum is 95 units.

If the gene is not imprinted we might expect it to produce about 100 units, with each allele producing 50. However, once the evolutionary dynamics of imprinting take over, the pattern of expression will evolve to one where alleles are transcriptionally silent when maternally inherited, but where a paternally expressed allele is making 105 units.

For a growth-suppressing gene, where increased expression actually reduces prenatal growth, we expect the opposite pattern, where alleles are silenced when paternally inherited, but are expressed when maternally inherited. This set of predictions – that imprinted growth enhancers will be paternally expressed, and imprinted growth suppressors will be maternally expressed – matches the empirically observed pattern by and large, although there are a few counterexamples that are not fully understood at the moment.

This pattern of allele silencing has been dubbed the "loudest voice prevails" principle. The phenotype evolves to the optimum of the allele favoring higher expression. Now, you can argue that this is the sort of thing that does not really need its own name. Fair enough. It's really just saying that the evolutionarily stable state of the system is an edge solution. But, "loudest voice prevails" is sort of catchy, and has the advantage of reminding us which allele is expressed at equilibrium.

The Haig 1996 citation is the paper that introduces the phrase. The other three citations are papers published around the same time that use different mathematical frameworks to address the evolution of gene expression at an imprinted locus. Generically speaking, the answer is the one described here, although the Spencer, Feldman, and Clark paper identifies certain regimes in parameter space where apparently different results can be obtained. In a future post, we will delve into the differences in the assumptions and conclusions of different modeling frameworks as they have been applied to imprinting.

Now, what if you consider more than one imprinted gene? What if Pat and Chris each have a space heater and an air conditioner? We'll talk about that next time.

[1] Of course, in the real-life situation, we might assume that Pat and Chris would discuss the situation and come to some sort of agreement. This is a key difference between people interacting in strategic situations and genes evolving under natural selection. Alleles at a locus are like people sharing an office, where both of them are incredibly passive aggressive. If it helps, imagine that Pat and Chris won't talk to each other.

[2] In practice, of course, there is going to be some minimum level of disagreement required in order to trigger this passive-aggressive escalation. In this analogy, the minimum level will be set by a combination of things such as the sensitivity of Pat and Chris to small changes in temperature, the precision with which the space heaters control the temperature of the room, and the extent to which they care about each other's comfort. Similar reasoning holds in the case of genes, and we will address this in a future installment of the series, where we ask why there are any genes that are not imprinted.

Thursday, January 13, 2011

So, Google has already had it's Twitter account subpoenaed, and can look forward to months of molestation enhanced screening at the airport, all thanks to its brazen violation of Benford's Law.

What is this Benford's Law thing?

It is a statement that if you look at lists of numbers in empirical data, the first non-zero digit is distributed in a very specific way. At least for certain kinds of data. Specifically, if the logarithms of the numbers you are looking at are uniformly distributed, then the first digits of those numbers will be Benfordly distributed.

Here's what the relative probabilities of different first digits look like:

Here's a graphic that shows the frequencies of different letters and numbers in Google searches. The numbers are way down at the bottom.

The thing that you'll notice about this is that 6 is by far the most common digit (and that J/j is sad). Here's a plot of these relative frequencies on the same scale as the Benford's Law plot above.

Roughly speaking, this plot has the same shape as the one above, except for the fact that it includes 0, and that 6 is crazy. But, look at where the 0 value is: pretty much even with where you might expect the 6 to be. What happens if we assume that this was actually a transcription error that happened somewhere along the way? If we switch the 6 and 0 values, and then look at the relative probabilities of all of the non-zero digits, we get this:

The dark blue dots are the Benford's Law points that we showed before. The reddish squares are the new empirical distribution.

Now that we've switched the 6 and the 0, we get something that looks to me like a mixture of the Benford's Law distribution and a uniform distribution. But remember, Benford's Law applies to first digits. This is data from all google searches. So, that's going to be a mixture of first digits and non-first digits.

If we assume that 35% of the non-zero digits in searches are first digits, and that the other 65% are uniformly distributed between 1 and 9, we can back out the relative frequencies of the digits specifically in the first digit context.

The blue circles are the Benford's Law expectations, and the red squares are the inferred empirical distribution of first digits. The choice of 35% was established through manual trial and error, and the fit was done by visual inspection. So, you know, don't go and make any medical decisions based on this.

This is actually a reasonably good fit for this sort of thing, and constitutes fairly compelling evidence in support of the "sumbudy dun messed up" theory to my mind. Either that, or you have to invoke roughly 6 billion instances of people googling '666'.

Frank Benford (1938). The law of anomalous numbers Proceedings of the American Philosophical Society, 78 (4), 551-572

So, gifted comedienne Cindy Jacobs has set the cyberverse aflame with her dead-on satirical portrayal of a manipulative, dishonest, bigoted snake-oil salesman. You may already have seen her outstanding video, which has been circulating the past few days. In it she spins a yarn about how the recent large-scale die-off of fish and birds in Arkansas are the result of the repeal of Don't Ask, Don't Tell.

For those of you who are not familiar with this particular brand of irony, let me break it down for you. You see, it paints this completely ridiculous picture of God as a homophobe with tendency to lash out, where he takes out his anger about homosexuals serving openly in the U. S. Miliatry on a bunch of defenseless animals. I actually worry a bit that she may have gone too far, and that this disrepectful portrayal may be viewed as blasphemous by some.

And she nails the pseudo-logic that these false prophets use. It's like something straight out of a Tina Fey skit. Here's a snippet:

. . . the blackbirds fell to the ground in Beebe, Arkansas. Well the Governor of Arkansas' name is Beebe. And also, there was something put out of Arkansas called "Don't Ask, Don't Tell," by a former Governor this was proposed – Bill Clinton.

Great stuff! And there's more. Like she's got a whole thing on how California will be destroyed by earthquakes if Prop 8 is repealed.

Back before the 2010 midterms, she had a skit about how if Latinos would support candidates who opposed gay marriage and abortion, God would reward them with comprehensive immigration reform. More Bible humor! See, it's just like the Book of Job. Elect right-wing candidates, and you get immigration "reform," like in Arizona.

Even her website is hilarious. She starts off with an oxymoronic description of herself as a "respected prophet." She then goes on to . . .

Wednesday, January 12, 2011

So, here is the debut of yet another new feature: Reflected Glory. This series will contain my callous and cynical attempts to convince you that this blog is really interesting and valuable because it is interested in and values interesting and valuable things.

To launch this feature, we have the math, music, and awesomeness blog of Vi Hart. You can get instructions on how to slice apples into Platonic Solids. You can listen to original stories set to original music. And you can watch the Doodling in Math Class video series, which covers things like how to draw an infinite line of camels such that they reach exactly to the edge of the page.

If you're a math geek, this is probably already bookmarked on your browser. If you're not, don't let that stop you from checking it out. The site is not about math in the sense of memorization, abstract notation, and jargon. It is about the beauty of patterns and music and fun. You'll want to spend plenty of time exploring.

The downside is that you will feel totally inadequate after seeing what this talented artist, composer, musician, mathematician, and expositor can do.

Tuesday, January 11, 2011

So, welcome to the first installment of Lost in Transcription's newest feature: The Genetical Book Review. For the maiden voyage, we'll cover the 2002, Pulitzer-prize-winning Middlesex by Jeffrey Eugenides.

You're surprised? Because you assume that an eight-year-old Pulitzer winner must already have been reviewed?

Fair enough. But, here's the gimmick: we'll use the genetics angle to talk about some things that have not already been covered extensively elsewhere.

First, though, the precis and value judgement. If you've not read the book, or read about it, it follows three generations of the Greek-American Stephanides family, who traipse through a slice of historical events in Smyrna and Detroit over the course of nearly a century. It's sort of a Forrest Gump for the NPR set. Cal Stephanides and his relatives witness genocide at the hands of the Turks, emigrate to America, build cars for Henry Ford, and run booze during prohibition. They are present for the founding of the Nation of Islam and the 1967 Detroit race riots. They flee to the suburbs and watch Watergate unfold on the television.

As in Forrest Gump, some of the historical context feels a bit like pandering, an attempt to draw the reader in through nostalgia. On the other hand, many of the events are local enough to be only passingly familiar to most readers, so there's learning to be had. More importantly, those events are always portrayed through the lens of how they shaped the trajectories of the characters in the book. And, they are charmingly and engagingly written, with a varied style that is pleasurable to read.

Basically, if your book group has not already read this book, and you're sick of plodding stories about alcoholic mothers and victims of sexual abuse, but want something with some literary gravitas (so that you don't lose social status by suggesting it to your book-group frenemies), this is the book for you!

So, this week at Lost in Transcription we'll be rolling out a few new features. The first of these is Well Thank God for THAT, which will cover some of those "current" "events."

If you haven't been to your local bookstore recently, you may have missed the fact that Simon Spotlight has published a novelization of Gulliver's Travels. Now a generation will not be deprived of this Jack Black classic during a power outage that is long enough for their laptops to run out of juice, but not so long that their kindles run out of juice.

If you've never read it, Gulliver's Travels offers an almost swiftian satire of human nature. It focuses particularly on two of our most enduring foibles: (1) being fat, and (2) saying "awesome" a lot.

Friday, January 7, 2011

So, one of the interesting things about having a website is that you can track the keywords that people Google that lead them to you. I get a lot of hits from people searching on "Jon Wilkins naked." It turns out that's not as exciting as it sounds. One of the other Jons Wilkins is one of the cofounders of the marketing firm Naked Communications. So, I assume that some fraction of those people were actually looking for him.

It got me interested, though, in the relative web presences of "Jon Wilkins" and "Jon Wilkins naked," and, by extension, in the relative naked and non-naked web presences of people in general. I'm going to call this the Negative Log Google Naked Ratio (NLGNR): the ratio of the number of hits when you Google "[Person's Name] naked" to the number of hits when you just Google "[Person's Name]" in log base 10. Negative.

Here's an example. When I searched for "Kanye West" today, Google found approximately 38,600,000 hits. I then searched for "Kanye West naked" and got approximately 428,000 hits. The ratio of these two is about 0.011088, and the logarithm base 10 of that is about –1.95.

So, Kanye West's NLGNR is 1.95.

If your NLGNR is 1, that means that 10% of all of the hits for your name actually come from pages where your name is followed by the word "naked." If your NLGNR is 2, it is one in a hundred pages. NLGNR of 3 means one in a thousand, and so on.

Just like in golf, low scores are better, assuming that your goal is to have your internet presence primarily associated with nakedness.

I did this for 93 people, and I have to tell you the internet is a weird place. Before presenting the whole chart, here are some of the highlights.

Top among the people I surveyed was Mia Hamm, whose NLGNR is an impressive 0.83. That means nearly 15% of the sites containing the phrase "Mia Hamm" contain the phrase "Mia Hamm naked." Weird? No. That actually seems low to me.

Thursday, January 6, 2011

So, today was the big day when the U. S. Constitution was read into the congressional record. This was preceded by a discussion of which parts, exactly, would be read. It was agreed that they would not read those sections of the Constitution that had been made irrelevant by amendments. That means, for instance, that they did not have to read all of the stuff about slaves.

And so, the Democrats lose again.

Why? Because the game being played here by the Republicans is part of the new Constitution-as-sacred-text push that is being fueled by the tea partiers. The founding fathers (sorry, I mean Founding Fathers) are being cast as infallible geniuses who set down immutably true principles of governance. Then, they can oppose any policy or piece of legislation on the moral principle that it is not what the Founding Fathers would have wanted.

The problem with reading the abridged Constitution is that it takes something that is a living, evolving entity and casts it as fixed. If the congress had read out all of the parts about slaves being three fifths of a person, and then read out the amendments abolishing slavery, the effect would have been the opposite. They would have emphasized that the Constitution as a document was not infallible. It would have emphasized the notion of the Constitution as a process.

The founding fathers were clever. They got a lot of things right. They also recognized that they were not going to get everything right, and that times and values would change.

I wish that they had read the entire Constitution into the congressional record. I am moved not by an America in which the government is something that we revere, but by an America in which the government is something that we do.

Wednesday, January 5, 2011

So, I'm reading teh Boing Boing the other day, and they have this article about Spokeo, which I assume is having a burst of coverage right now because its founder, Harrison Tang, was just elected Grand Sucktard of Douchebekistan.

This is a "service" where you can type in your name (or presumably the name of someone you want to rob, terrorize, and/or murder), and it will show you a satellite image of their house, along with a bunch of personal information about things like number of children and estimated wealth.

Just how much of a wankwad is this Tang dude? As Boing Boing point out, "Tellingly, Mr. Tang opted out of his own site over privacy concerns."

A full set of instructions on how to opt yourself out can be found here. I clicked on the privacy button, and was greeted by the statement that "Spokeo cares about data privacy." You can then have yourself removed from Spokeo's public searches (although presumably not from their database) "for free."

BUT, they are quick to point out, YOUR PRIVACY IS STILL AT RISK!!1!11! Your information will still be available through other sites, and you will have to contact them "one-by one . . . to protect your online identity."

Fortunately, the heroes at Spokeo have "partnered with" the company "Reputation Defender," which will protect your online identity for a modest fee. What I'm wondering is, what's the deal with that? Is that Spokeo's actual business model? How is this any different from having the guy who threatens your family "partner with" Vito Corleone?

I'm not breaking any news here. I just wanted to post something because I thought that the protection-racket aspect of this whole thing did not receive enough emphasis in the article by Boing Boing's Xeni. Not a complaint, as that article had a somewhat broader point, and is a great read for anyone interested in online privacy issues.

Also, I had about a million HILARIOUS ways to misspell "Harrison Tang", but then decided to spare you.

Tuesday, January 4, 2011

So, if you haven't already, you'll probably soon receive the credit card bill with all of your Christmas purchases on it. Was it worth it? Well, was it, punk?

If you're like most people, some of your presents were probably intended to impress someone. The question is, what's the best kind of present for that? Should I give the girl from math class diamond earrings, or new batteries for her calculator? Should I give my boss a mug, or a gift certificate to Glamour Shots?

Fortunately, Science!™ has the answer. Today's journal club entry concerns a model of gift-giving that considers three different types of gift that differ in their cost to the giver and their value to the recipient. "Cheap" gifts are, well, cheap. "Valuable" gifts are expensive to give, and have value to the recipient. The interesting category is the third one, the "extravagant" gifts, which are expensive to give, but have little inherent value to the recipient.

The specific context is gift-giving and mating. The model is of a sequential game with three or four stages. First, the male offers a gift to the female. Second, the female either accepts or rejects the gift. Third, she chooses whether or not to mate with the male. Then, in one version of the game, the male decides whether or not to stick around and contribute to the care of the offspring.

The conclusion of the paper is that there are many combinations of parameter values that will lead to males giving extravagant gifts. There are two critical features of the model that seem to be necessary in order to get this result.

First, there is uncertainty. The female has a guess about the quality of the male (or, equivalently, in the version of the model with paternal care, the probability that he will stick around after mating). By accepting the gift, she gains additional information about his quality or intentions. Similarly, the male is uncertain about the quality and intentions of the female – whether it is worth it for him to stick around after mating, and whether or not she is a gold-digger, who will just take his gift and skip town with his cousin.

[Editorial note: the term "gold-digger" is from the paper. Those of you who know me know me know that I would never have gone with such a politically incorrect term. I would have used "■■■■■■■■■■".]

[[Meta-editorial note: parts of the previous editorial note have been redacted.]]

The other key feature is that there must be some cost to the female in accepting the gift.

Now, there are lots of parameters in a model like this, and several equilibrium solutions are possible. The interesting one is the one where males give cheap gifts to unattractive females (females whom they judge, with some uncertainty, to be of low quality), and give extravagant gifts to attractive females.

The key to getting the interesting equilibrium is that the ability or willingness to provide and extravagant gift has to correlate with the male's quality or intentions. For example, a male can't afford to spend two-months salary on a diamond ring every time he wants to have a one-night stand. Therefore, an extravagant engagement ring becomes a reliable indicator of his intentions. Ideally, the gift has to have no inherent value to the female, for example, if it were impossible to sell the engagement ring for cash money. Recall also that it has to cost her something to accept the gift. Then, taking the gift constitutes a commitment on her part as well. Otherwise, she benefits most from accepting the gift and walking away.

In the salacious application-to-human-mating case, this cost to the female is easiest to envision as a reputation cost (e.g., the risk of being labeled as a ■■■■■■■■■■). In certain species, where females mate with multiple males, store the sperm, and then use it selectively, there may be direct opportunity costs that do not require catty moralizing.

Just one last point.

The paper starts with, "Gift-giving is a feature of human courtship". The authors cite Geoffrey Miller's 2000 book, The Mating Mind. If the paper were being written today, I assume they would have cited more recent work by Hefner and Harris.

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